Some apps and settings/storage see my SD card, but most dont.

Need a bit of help here, have an mtk6572 no mark phone on 4.2, works perfectly. Changed rom to an also 4.2 which runs a lot quicker and is themed etc...
All is good except the sd card, android system sees it, root explorer sees it, gallery sees it, gramaphone sees it but...
camera doesnt, osmand maps doesnt, browser doesnt, swiftkey doesnt etc. CWM and windows see it and can format it so have done that in fat/fat32/ntfs as well as mounting before booting but still the same thing happens. Restore my old backup and all is back to normal. Have checked the new rom updater-script and I have the mounts correct number wise, same as the working rom and now I'm all out of ideas :(

Any ideas guys?

Thanks.